Aetherytes, Garleans, and You!

[Enkidoh]

I thought they flew directly in. It's been a really long time since I watched the 2.0 story, though, but I'd always imagined that they dropped directly into Vesper Bay with a small airship, and left the same way. Otherwise it raises the question of how they got their Scion prisoners out of there as well.

When the player first arrives outside the Waking Sands in that scene a crowd of villagers is clustered around outside who state they've all heard screaming coming from inside but saw nothing else. A Garlean airship, even a small one, would kind of be noticeable if it landed in the middle of a major port town like Vesper Bay (to say nothing of an Immortal Flames encampment literally next door to the place would have immediately rushed to it's defense if that had been the case.) But all that was known was suddenly there was a commotion inside that was heard by everyone outside, but no one knew exactly what was happening:

Disquieted Villager (outside the Waking Sands): "You hear that commotion just now? What in the seven hells were they doin' in there? Wrestlin' a peiste!? You look like the adventurin' type. Mind taking a quick look?"
Frightened Villager: "...Was that screaming I heard? I'm not sure I want to know..."

In fact, even why the Garleans were even there (to try and capture the player's character) clued Minfilia in that this was no ordinary raid - that they had infiltrated the place magically instead of by mundane means (Livia naturally waves her thought aside). So Lahabrea teleporting the Garleans in and then out with their Scion prisoners is the only logical way that they could have infiltrated the Waking Sands without anyone outside noticing.